Pig genome annotation: A Gene Wish List

A Wish List of Genes for Annotation (version 3.26)

(Matches to BACs by their Genome Locations Based on Pig Genome Build v.9 (Data Downloads as of Mar. 7, 2010 )

Info:

Purpose: Help users to find where to go from gene names to their genome locations/BACs in order to locate a starting spot in the pig genome to bring into Otterlace for annotations.
Methods: The gene locations are determined in 2 ways: Ensembl predictions and Blasts. Clones are sought based on their overlapping genome locations with that of your gene.
Terms: Finished BACs: A total of 811 "finished" clones that met the "golden standard" of finished sequencing quality. Unfinished clones: Out of 15,837 clones on the "unfinished clones" list, only 1,769 have been processed to have genome locations. FPC clones: 254K+ of those clones in the sequencing pipeline
Related links:

HINTS:

Owner/Status info: : Someone has this gene on their wish-list to annotate. : This gene is to be annotated. : This gene has been annotated (click to check for details - maybe only a gene variant is annotated. The ultimate annotator list is from Otterlace entries; This list only provides a working reference).
Additional info: : have orthologous gene information. : have refseq information. : details (click for more)
Ensembl Gene ID, Genome Locations, and BAC names are all hyper-linked to Ensembl database

( Go to genes whose symbol start with: 1, 5, 7, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z )
Search results:	Show Finished BAC Show unFinished BAC

User Gene List			Genome Location (Chr.:start-end)	Fell within Finished BACs (Contig, BACname, Chr.:Start-End)	Fell within Unfinished Clones (SeqName, Chr.:Start-End)
Symbol	Owner/ Status	Ensembl Gene ID	Genome Location (Chr.:start-end)	Fell within Finished BACs (Contig, BACname, Chr.:Start-End)	Fell within Unfinished Clones (SeqName, Chr.:Start-End)

ADAM2		location ⇒	15:44508488-44508673		CU570964,CH242-96G4,15:44491114-44509901 (Clone quality: bE96G4 on chr=15; Num_of_Contigs=11; )
ADAM2		location ⇒	15:44535092-44535337		FP236144,CH242-340E24,15:44525538-44542668 (Clone quality: bE340E24 on chr=15; Num_of_Contigs=3; )
ADAM2		location ⇒	15:44658026-44657829		FP236144,CH242-340E24,15:44639599-44658724 (Clone quality: bE340E24 on chr=15; Num_of_Contigs=3; )
ADAM22		ENSSSCG00000015297	9:63795434-63877489		CU633545,CH242-158M1,9:63744168-63879804 (Clone quality: bE158M1 on chr=9; Num_of_Contigs=1; )
Adam23		ENSSSCG00000009644	14:8405767-8473344
ADAM23		ENSSSCG00000009644	14:8405767-8473344
Adam23		ENSSSCG00000016131	15:102464691-102650958
ADAM23		ENSSSCG00000016131	15:102464691-102650958
Adam23		location ⇒	15:102464827-102464904		CU467535,CH242-21E18,15:102428219-102471324 (Clone quality: bE21E18 on chr=15; Num_of_Contigs=4; )
Adam23		location ⇒	15:102579984-102580065		CU694854,CH242-241I15,15:102506891-102618348 (Clone quality: bE241I15 on chr=15; Num_of_Contigs=6; )
Adam23		location ⇒	15:102620325-102620419		CU694854,CH242-241I15,15:102618449-102640689 (Clone quality: bE241I15 on chr=15; Num_of_Contigs=6; )
ADAM23		location ⇒	15:102625574-102625746		CU694854,CH242-241I15,15:102618449-102640689 (Clone quality: bE241I15 on chr=15; Num_of_Contigs=6; )
ADAM23		location ⇒	15:102628745-102629011		CU694854,CH242-241I15,15:102618449-102640689 (Clone quality: bE241I15 on chr=15; Num_of_Contigs=6; )
Adam23		location ⇒	15:102738569-102738663		FP102081,CH242-27H24,15:102733622-102742681 (Clone quality: bE27H24 on chr=15; Num_of_Contigs=11; )
ADAM23		location ⇒	15:102743625-102743796		FP102081,CH242-27H24,15:102742782-102754133 (Clone quality: bE27H24 on chr=15; Num_of_Contigs=11; )
ADAM23		location ⇒	15:102746795-102747061		FP102081,CH242-27H24,15:102742782-102754133 (Clone quality: bE27H24 on chr=15; Num_of_Contigs=11; )
ADAM28		ENSSSCG00000009644	14:8405767-8473344
ADAM28		location ⇒	14:8435873-8436044		CT954207,CH242-1L13,14:8427685-8604674 (Clone quality: bE1L13 on chr=14; Num_of_Contigs=1; )
ADAM28		location ⇒	14:8439568-8439653		CT954207,CH242-1L13,14:8427685-8604674 (Clone quality: bE1L13 on chr=14; Num_of_Contigs=1; )
ADAM28		location ⇒	14:8448501-8448635		CT954207,CH242-1L13,14:8427685-8604674 (Clone quality: bE1L13 on chr=14; Num_of_Contigs=1; )
ADAM28		location ⇒	14:8449893-8450073		CT954207,CH242-1L13,14:8427685-8604674 (Clone quality: bE1L13 on chr=14; Num_of_Contigs=1; )
ADAM29		ENSSSCG00000009697	14:14907296-14909365		CU468446,CH242-93F8,14:14893916-14943456 (Clone quality: bE93F8 on chr=14; Num_of_Contigs=6; )
ADAM30		ENSSSCG00000006713	4:105556721-105558895		CU468974,CH242-143C13,4:105549404-105573357 (Clone quality: bE143C13 on chr=4; Num_of_Contigs=10; )
ADAM32		ENSSSCG00000015807	15:44738776-44882301
ADAM7		location ⇒	14:8540268-8540445		CT954207,CH242-1L13,14:8427685-8604674 (Clone quality: bE1L13 on chr=14; Num_of_Contigs=1; )
ADAM7		location ⇒	14:8543765-8543963		CT954207,CH242-1L13,14:8427685-8604674 (Clone quality: bE1L13 on chr=14; Num_of_Contigs=1; )
ADAM7		location ⇒	14:8687061-8687238		CU407140,CH242-142M6,14:8662992-8730207 (Clone quality: bE142M6 on chr=14; Num_of_Contigs=9; )
ADAM7		location ⇒	14:8690558-8690756		CU407140,CH242-142M6,14:8662992-8730207 (Clone quality: bE142M6 on chr=14; Num_of_Contigs=9; )
ADAM8		ENSSSCG00000010772	14:147966527-147977088
ADAM8		location ⇒	14:147967088-147967004		CU468487,CH242-34M16,14:147937769-147975182 (Clone quality: bE34M16 on chr=14; Num_of_Contigs=8; )
ADAM8		location ⇒	14:147969433-147969246		CU468487,CH242-34M16,14:147937769-147975182 (Clone quality: bE34M16 on chr=14; Num_of_Contigs=8; )
ADAM8		location ⇒	14:147970045-147969927		CU468487,CH242-34M16,14:147937769-147975182 (Clone quality: bE34M16 on chr=14; Num_of_Contigs=8; )
ADAM8		location ⇒	14:147970734-147970649		CU468487,CH242-34M16,14:147937769-147975182 (Clone quality: bE34M16 on chr=14; Num_of_Contigs=8; )
ADAM9		ENSSSCG00000015808	15:44886862-45167936
ADAM9		location ⇒	15:44910864-44910786		CU469515,CH242-238L24,15:44884786-44988021 (Clone quality: bE238L24 on chr=15; Num_of_Contigs=5; )
ADAM9		location ⇒	15:44914194-44914088		CU469515,CH242-238L24,15:44884786-44988021 (Clone quality: bE238L24 on chr=15; Num_of_Contigs=5; )
ADAM9		location ⇒	15:44917789-44917593		CU469515,CH242-238L24,15:44884786-44988021 (Clone quality: bE238L24 on chr=15; Num_of_Contigs=5; )
ADAM9		location ⇒	15:44918886-44918809		CU469515,CH242-238L24,15:44884786-44988021 (Clone quality: bE238L24 on chr=15; Num_of_Contigs=5; )
ADAMDEC1		ENSSSCG00000009645	14:8489941-8504411		CT954207,CH242-1L13,14:8427685-8604674 (Clone quality: bE1L13 on chr=14; Num_of_Contigs=1; )
ADAMDEC1		location ⇒	14:8490324-8490445		CT954207,CH242-1L13,14:8427685-8604674 (Clone quality: bE1L13 on chr=14; Num_of_Contigs=1; )
ADAMDEC1		location ⇒	14:8491329-8491408		CT954207,CH242-1L13,14:8427685-8604674 (Clone quality: bE1L13 on chr=14; Num_of_Contigs=1; )
ADAMDEC1		location ⇒	14:8493682-8493760		CT954207,CH242-1L13,14:8427685-8604674 (Clone quality: bE1L13 on chr=14; Num_of_Contigs=1; )
ADAMDEC1		location ⇒	14:8495063-8495211		CT954207,CH242-1L13,14:8427685-8604674 (Clone quality: bE1L13 on chr=14; Num_of_Contigs=1; )
ADAMTS1		ENSSSCG00000012026	13:135954679-135959764
ADAMTS12		ENSSSCG00000016816	16:16920947-17221603
ADAMTS12		location ⇒	16:16869812-16869479		FP085401,CH242-267F2,16:16867905-16877148 (Clone quality: bE267F2 on chr=16; Num_of_Contigs=5; )
ADAMTS12		location ⇒	16:16889507-16889350		FP085401,CH242-267F2,16:16887919-16925320 (Clone quality: bE267F2 on chr=16; Num_of_Contigs=5; )
ADAMTS12		location ⇒	16:17054981-17054648		FP236528,CH242-231C7,16:17054232-17057507 (Clone quality: bE231C7 on chr=16; Num_of_Contigs=18; )
ADAMTS12		location ⇒	16:17133784-17133627		FP236528,CH242-231C7,16:17131888-17138438 (Clone quality: bE231C7 on chr=16; Num_of_Contigs=18; )
ADAMTS14		ENSSSCG00000010272	14:76771145-76804964

Go to records:
1-49, 50-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-450, 451-500, 501-550, 551-600, 601-650, 651-700, 701-750, 751-800, 801-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-32

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$version: 3.26; Updates: Mar. 6, 2010; Apr. 20, 2010; Aug 21, 2010

Related publications:

Martien Groenen, Alan Archibald, Hirohide Uenishi, Christopher Tuggle, Yasuhiro Takeuchi, Max Rothschild, Claire Rogel-Gaillard, ... Denis Milan, Hendrik-Jan Megens, ... Zhi-Liang Hu, Sean J. Humphray, ... James M. Reecy, ..., Gary A. Rohrer, ... Shuhong Zhao, Jane Rogers, Carol Churcher & Lawrence B. Schook. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491, 393-398 (15 November 2012).